| 2 essential parts of Darwins Theory | 1 Common descent 2 Mechanisms of selection and mutation |
| Traditional Classification by Linne, Cuvier | Observation of nested character states, no subdivision between old and derived, binomial classification |
| Likelihood of transmission of ontogenetic information across generations depends on | Adaptive traits, sexual selection (no. of offspring) and chance |
| Von Baer's Law | Larval stages are often very similar to each other than adult stages |
| Evolution is chain of ontogenies | Common ancestor had processes in place that led to similar features in descendants |
| What is a character? | Any assayable feature carried at high freq in pop, not all are useful but the synapomorphic ones (by Hennig) |
| Relative terms in triad | Sister groups , outgroups, paraphyletic grouping: does not include all descendants of a common ancestor, (syn)apomorphy: new character only shared between sister groups and plesiomorphy: older character shared by several taxa |
| Monophyletic group, Stem group | Monophyletic group = group of all taxa derived from a common ancestor, including this ancestor
Stem group = ancestral taxon of monophyletic group not shared with other monoph grouping |
| Computational approaches to calculate parsimonious trees | 1 Calculate Matrix Q 2 Find the pair taxa with the lowest Matrix Q value 3 Create a node to join the two taxa 4 Calculate distance of each pair taxa to new node 5 Calculate distance of every taxa to node 6 start algorithm again |
| Adding fossils to taxa | They give info about the state and transition of a character
1 Establish a tree with monophyletic groups
2 Map characters into a tree and infer from outgroups primitive conditions
3 Extend knowledge by mapping older taxa
More character info can change the polarity of character changes |
| Total groups | Include the crown group of interest plus all extinct forms more closely related to that lineage than any other living species
Crown group = the last common ancestor of a group of living species plus all of its descendants. |
| Character Evolution | 1 Establish a pasrimonious set of equally likely trees on a large set of features
2 Map characters and their changes onto the tree
3 Determine the molecular mechanisms underlying these changes |
| Extant phylogenetic bracket | Inferential tool when dealing with inaccessible organisms |
| ow can we trace the sources of similarity/homology? | Study character evolution use plesiomorphic genetic features to label common (homologous) populations of cells |
| Constraints on mutational change: forces of conservation | Developmental or genetic coupling of different features as their development uses the same genes and pathways.
Common cell pops
Important genes do not get modulated much through mutations |
| Hox genes | Vertebrae types directly correlate with the prior gene expression domains of Hox genes across different vertebrate species, thus changes in expression domains could generate diverse morphologies.
First expressed in the CNS, somites and unpaired fins; Paired fins evolved after unpaired fins
Later in evolution Hox gene codes are coopted to the paired fins and are used to subdivide them molecularly; Cooption of a molecular programme from one body region to another! |
| Digits | The expression domain of the HoxD13 paralogs
Sets up the territory for digits of the autopod!
Shifts in that domain in evolution change number and shape of digits.
These shifts are part of the second wave of hox expression |
| Hox genes pt 2 | Collinearity of hox gene = Position + time and space of gene expression
Cooption of rested hox gene expression into paired appendages
Cluster position determines proximo-distal position and timing of expression
Late expression domains are used for the formation of digits
Changing of Hox and GLi gene dosage, change the digit numbers
Re-use of hox genes in therian mammalians to differentiate reproductive organs |
| Mechanistic concept underpinning character evolution | CRMs (cis-regulatory modules, enhancers, silencers) Modular control units of gene expression |
| Homology - conservation of developmental programmes | What stays the same. Inherited trait from common ancestor due to inherited process of generating that trait |
| Tinkering with ontogeny leads to | Changes in developmental timing of individual sub-programmes and ensuing structures. Deviation, addition of ontogenetic end stages. Paedomorphosis and neoteny, adult of descendant like juvenile by 1 acceleration of sexual maturation while somatic maturation is constant 2 delay in somatic maturation while sexual maturation stays constant 3 Loss of end stages of ontogeny |
| Coenogenesis | Larval specializations and how to resolve complex character changes. |
| Heterochrony | Change speed of development |
| Modularity: forelimbs vs hindlimbs | Tbx5 specifies forelimb, Tbx4 specifies hindlimb characteristics. They are controlled by Hox genes along the AP body axis! |
| Deviation | Elaboration of early programme by changing end stages: gripping hand, opposable thumb.
Temporal axis turns into physical axis: digits form and individualize last!
Late blockage will prevent individuation of fingers – yielding paddles/flippers! |
| The developmental hourglass and phylotypic stage | Quantifying genetic processes for each developmental stage.
There are certain stages in which highly conserved gene networks are active across many related species - the phylotypic stage/period |
| Phylostratigraphic maps | Assign ages to genes
Ranks them
gives them weighting |
| Hourglass: The transcriptome age index (TAI) | Determine which age are most active |
| The most basic elements of gene regulation and its change | Pax and Otx transcription factors
CRMs - Heterochrony, boxes of DNA with highly conserved binding sites with transcription factors |
| Body appendages | All appendages depend on Dll (distalless) gene action
BUT the instructions of how many legs an animal has evolved independently.
Butterfly eyespots re-utilize a gene wingless that makes appendages. Wingless activates Distalless (DLL) to make the eye spot |
| Pax6 | Pax6 cooptions for vision and brain Formation – making master predators
Photopigment cell Photoreceptor cell gene and protein network already existed In our coral-like ancestor
Cooption of a Pax6 programme to other body regions making many eyes in the ectodermal tissues |
| Exon shuffling and lateral gene transfer Pax 6 | Ancient cyanobacterial transposase. Hitched from a dinoflagellate alga – was related to transposases! Paired domain of Pax6 derived from DNABD of the TC1 transposon; lateral gene transfer has moved Pax6 to diploblastic hosts |
| Exon shuffling to generate evolutionary novetlies | Enormous gain of introns, exon shuffling as mechanism to generate novelty, Evolution of Notch and hedgehog signalling molecules, evolution of collagen |
